SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041627_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.2 Cutadapt version: 2.6 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp File was specified to be an MspI-digested RRBS sample. Read 1 sequences with adapter contamination will be trimmed a further 2 bp from their 3' end, and Read 2 sequences will be trimmed by 2 bp from their 5' end to remove potential methylation-biased bases from the end-repair reaction All Read 2 sequences will be trimmed by 2 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 3 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 3 bp from their 3' end to avoid poor qualities or biases Output file will be GZIP compressed This is cutadapt 2.6 with Python 3.6.7 Command line parameters: -j 1 -e 0.1 -O 1 -a AGATCGGAAGAGC /sibcb2/bioinformatics2/heshutao/processing/cup/BS_workflow/20201120/tmp/a59f7e8c-5572-11eb-92c8-6c92bfbaf176/trimmed/RRBS20A041627_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 159.20 s (23 us/read; 2.66 M reads/minute). === Summary === Total reads processed: 7,046,374 Reads with adapters: 2,879,713 (40.9%) Reads written (passing filters): 7,046,374 (100.0%) Total basepairs processed: 704,516,116 bp Total written (filtered): 682,461,632 bp (96.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2879713 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 27.8% C: 0.9% G: 24.8% T: 46.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1980096 1761593.5 0 1980096 2 575682 440398.4 0 575682 3 132635 110099.6 0 132635 4 30364 27524.9 0 30364 5 1657 6881.2 0 1657 6 1081 1720.3 0 1081 7 614 430.1 0 614 8 560 107.5 0 560 9 861 26.9 0 776 85 10 848 6.7 1 339 509 11 603 1.7 1 100 503 12 269 0.4 1 62 207 13 325 0.1 1 67 258 14 612 0.1 1 92 520 15 434 0.1 1 85 349 16 1100 0.1 1 189 911 17 1294 0.1 1 277 1017 18 881 0.1 1 336 545 19 37 0.1 1 1 36 20 307 0.1 1 46 261 21 47 0.1 1 3 44 22 81 0.1 1 17 64 23 276 0.1 1 46 230 24 929 0.1 1 185 744 25 380 0.1 1 79 301 26 165 0.1 1 24 141 27 410 0.1 1 75 335 28 897 0.1 1 181 716 29 824 0.1 1 151 673 30 221 0.1 1 42 179 31 79 0.1 1 8 71 32 416 0.1 1 78 338 33 699 0.1 1 120 579 34 757 0.1 1 141 616 35 424 0.1 1 71 353 36 343 0.1 1 60 283 37 663 0.1 1 134 529 38 139 0.1 1 29 110 39 110 0.1 1 26 84 40 504 0.1 1 107 397 41 436 0.1 1 91 345 42 623 0.1 1 134 489 43 967 0.1 1 177 790 44 207 0.1 1 36 171 45 478 0.1 1 91 387 46 186 0.1 1 30 156 47 340 0.1 1 67 273 48 854 0.1 1 185 669 49 59 0.1 1 8 51 50 426 0.1 1 81 345 51 115 0.1 1 27 88 52 108 0.1 1 14 94 53 325 0.1 1 55 270 54 1210 0.1 1 262 948 55 670 0.1 1 121 549 56 293 0.1 1 56 237 57 526 0.1 1 102 424 58 302 0.1 1 51 251 59 118 0.1 1 18 100 60 242 0.1 1 42 200 61 357 0.1 1 52 305 62 970 0.1 1 192 778 63 283 0.1 1 51 232 64 31 0.1 1 4 27 65 18 0.1 1 0 18 66 87 0.1 1 10 77 67 119 0.1 1 29 90 68 529 0.1 1 106 423 69 517 0.1 1 93 424 70 912 0.1 1 190 722 71 339 0.1 1 68 271 72 114 0.1 1 17 97 73 196 0.1 1 40 156 74 188 0.1 1 44 144 75 261 0.1 1 48 213 76 241 0.1 1 45 196 77 244 0.1 1 43 201 78 275 0.1 1 62 213 79 213 0.1 1 41 172 80 307 0.1 1 54 253 81 270 0.1 1 66 204 82 296 0.1 1 65 231 83 298 0.1 1 49 249 84 225 0.1 1 52 173 85 257 0.1 1 67 190 86 331 0.1 1 64 267 87 201 0.1 1 54 147 88 131 0.1 1 29 102 89 201 0.1 1 39 162 90 174 0.1 1 41 133 91 187 0.1 1 41 146 92 149 0.1 1 34 115 93 525 0.1 1 152 373 94 740 0.1 1 139 601 95 189 0.1 1 38 151 96 144 0.1 1 34 110 97 937 0.1 1 240 697 98 105 0.1 1 29 76 99 71 0.1 1 14 57 100 82 0.1 1 18 64 101 77 0.1 1 15 62 102 122 0.1 1 27 95 103 51 0.1 1 11 40 104 37 0.1 1 7 30 105 25 0.1 1 5 20 106 20 0.1 1 4 16 107 15 0.1 1 3 12 108 5 0.1 1 1 4 109 5 0.1 1 1 4 110 5 0.1 1 0 5 111 5 0.1 1 0 5 112 2 0.1 1 2 114 2 0.1 1 0 2 116 8 0.1 1 2 6 117 1 0.1 1 0 1 118 1 0.1 1 0 1 122 1 0.1 1 0 1 123 2 0.1 1 0 2 124 1 0.1 1 1 126 3 0.1 1 1 2 127 4 0.1 1 3 1 128 1 0.1 1 1 129 3 0.1 1 1 2 130 4 0.1 1 4 131 5 0.1 1 4 1 132 9 0.1 1 9 133 19 0.1 1 11 8 134 27 0.1 1 24 3 135 42 0.1 1 37 5 136 105 0.1 1 90 15 137 8702 0.1 1 8502 200 138 111578 0.1 1 108728 2850 139 1 0.1 1 0 1 140 2 0.1 1 0 2 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/cup/20201120/RRBS20A041627_val_1.fq.gz ============================================= 7046374 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 271805 (3.9%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 2879713 (40.9%)